broad.pda.samtools.PairedEndTDF Class Reference

Inheritance diagram for broad.pda.samtools.PairedEndTDF:

Collaboration diagram for broad.pda.samtools.PairedEndTDF:

Public Member Functions
void	extendPairedEndReads (final File inSamOrBam, final File outSamOrBam) throws Exception

Static Public Member Functions
static void	main (final String[] args)

Public Attributes
String	USAGE
File	INPUT
File	OUTPUT
int	WINDOW = 25
String	GENOME = "mm9"
boolean	KEEP_INTERMEDIATE = false
boolean	INCLUDE_DUPLICATES = false
int	MAX_INSERT = 2000

Protected Member Functions
int	doWork ()
String[]	customCommandLineValidation ()

Detailed Description

Author

engreitz September 9, 2012

Member Function Documentation

String [] broad.pda.samtools.PairedEndTDF.customCommandLineValidation ( )

protected

int broad.pda.samtools.PairedEndTDF.doWork ( )

protected

Here is the call graph for this function:

void broad.pda.samtools.PairedEndTDF.extendPairedEndReads	(	final File	inSamOrBam,
		final File	outSamOrBam
	)		throws Exception

Here is the caller graph for this function:

static void broad.pda.samtools.PairedEndTDF.main ( final String[]  args )

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

String broad.pda.samtools.PairedEndTDF.GENOME = "mm9"

boolean broad.pda.samtools.PairedEndTDF.INCLUDE_DUPLICATES = false

File broad.pda.samtools.PairedEndTDF.INPUT

boolean broad.pda.samtools.PairedEndTDF.KEEP_INTERMEDIATE = false

int broad.pda.samtools.PairedEndTDF.MAX_INSERT = 2000

File broad.pda.samtools.PairedEndTDF.OUTPUT

String broad.pda.samtools.PairedEndTDF.USAGE

Initial value:

=
                "Converts a paired-end SAM or BAM file to a TDF file for IGV,\ncounting coverage by fragments instead of individual reads.\n"

int broad.pda.samtools.PairedEndTDF.WINDOW = 25

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The documentation for this class was generated from the following file:

• java/broad/pda/samtools/PairedEndTDF.java